The thing that pushes Storm 3 over Gen for me personally is Konan having a faster first hit & a buffed tilt, hidan & pts gaara having nerfed jutsu assist wise, & being able to stop & guard instantly after a chakra dash by pushing the guard button instead of having that awkward cool down where you can't sub.
Selfish reasons yes, but whatever, Storm 3 wins for those 3 specific reasons to me. I can more or less play around most other flaws. As long as i have Konan...
It's fun to see people talking about gameplay in a series where gameplay had always been the weaker point of the whole product. Hoping that we'll see a REAL fighting game next time, and not that button mashing and spamming crap, i vote Storm 3 because Storm Generation hasn't even a story mode. Better gameplay? That's not a gameplay, i told you.
I don't care about the boss fights. They were OK the first time around, but after that I lost interest in them.
I miss several of the left/right combos that were dropped in storm 3.
I STRONGLY dislike the IAs. (Admittedly this is because I tend to play as Kakashi, Jiraiya, or Shikamaru as they are my favorite characters from the manga and none of them has an exploitable IA)
But the main reason I prefer Gens is because of its roster. There IS a higher number of characters in Storm 3, but that number is inflated by clones. Plus Gens has almost all of the PTS characters, while Storm 3 has very few.
Again, these are simply my opinions, and if you happen to disagree with them, then I won't hold it against you.